Starting phenix.real_space_refine on Thu Feb 5 23:02:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmp_62440/02_2026/9kmp_62440.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 7995 2.51 5 N 2080 2.21 5 O 2395 1.98 5 H 7960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20465 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Restraints were copied for chains: C, E, G, H, D, F, I, J Time building chain proxies: 3.15, per 1000 atoms: 0.15 Number of scatterers: 20465 At special positions: 0 Unit cell: (120.52, 118.68, 82.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 2395 8.00 N 2080 7.00 C 7995 6.00 H 7960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.30 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.30 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.30 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.30 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.30 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 631.6 milliseconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 30 sheets defined 7.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.217A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 42 through 46 removed outlier: 4.217A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 42 through 46 removed outlier: 4.217A pdb=" N SER E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 169 through 177 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 42 through 46 removed outlier: 4.217A pdb=" N SER G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 169 through 177 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'H' and resid 42 through 46 removed outlier: 4.217A pdb=" N SER H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 169 through 177 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 4.271A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 101 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 108 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 99 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.818A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 53 removed outlier: 5.776A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.816A pdb=" N VAL B 14 " --> pdb=" O SER B 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.741A pdb=" N TRP B 37 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET B 35 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 34 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 99 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 120 removed outlier: 4.271A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 101 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 108 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 99 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.818A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 53 removed outlier: 5.776A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.816A pdb=" N VAL D 14 " --> pdb=" O SER D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.740A pdb=" N TRP D 37 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET D 35 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA D 34 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 99 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 118 through 120 removed outlier: 4.271A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU E 101 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 108 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 99 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 133 through 135 removed outlier: 3.818A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 53 removed outlier: 5.776A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 7 through 9 Processing sheet with id=AB8, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.817A pdb=" N VAL F 14 " --> pdb=" O SER F 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.741A pdb=" N TRP F 37 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU F 51 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET F 35 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA F 34 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 99 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 118 through 120 removed outlier: 4.271A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 101 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 108 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER G 99 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR G 34 " --> pdb=" O MET G 161 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET G 161 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS G 36 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL G 159 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 135 removed outlier: 3.818A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 49 through 53 removed outlier: 5.776A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 7 through 9 Processing sheet with id=AC5, first strand: chain 'I' and resid 14 through 15 removed outlier: 6.816A pdb=" N VAL I 14 " --> pdb=" O SER I 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.741A pdb=" N TRP I 37 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU I 51 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET I 35 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA I 34 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG I 99 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 118 through 120 removed outlier: 4.270A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU H 101 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU H 108 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 99 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 133 through 135 removed outlier: 3.819A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 49 through 53 removed outlier: 5.776A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 7 through 9 Processing sheet with id=AD2, first strand: chain 'J' and resid 14 through 15 removed outlier: 6.816A pdb=" N VAL J 14 " --> pdb=" O SER J 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.741A pdb=" N TRP J 37 " --> pdb=" O ALA J 49 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU J 51 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET J 35 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA J 34 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG J 99 " --> pdb=" O ALA J 34 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7960 1.02 - 1.21: 15 1.21 - 1.41: 5341 1.41 - 1.61: 7399 1.61 - 1.81: 50 Bond restraints: 20765 Sorted by residual: bond pdb=" C ARG I 21 " pdb=" N LEU I 22 " ideal model delta sigma weight residual 1.328 1.224 0.104 1.37e-02 5.33e+03 5.82e+01 bond pdb=" C ARG J 21 " pdb=" N LEU J 22 " ideal model delta sigma weight residual 1.328 1.224 0.104 1.37e-02 5.33e+03 5.80e+01 bond pdb=" C ARG B 21 " pdb=" N LEU B 22 " ideal model delta sigma weight residual 1.328 1.224 0.104 1.37e-02 5.33e+03 5.78e+01 bond pdb=" C ARG D 21 " pdb=" N LEU D 22 " ideal model delta sigma weight residual 1.328 1.224 0.104 1.37e-02 5.33e+03 5.77e+01 bond pdb=" C ARG F 21 " pdb=" N LEU F 22 " ideal model delta sigma weight residual 1.328 1.224 0.104 1.37e-02 5.33e+03 5.74e+01 ... (remaining 20760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.43: 35420 5.43 - 10.86: 70 10.86 - 16.29: 5 16.29 - 21.71: 0 21.71 - 27.14: 15 Bond angle restraints: 35510 Sorted by residual: angle pdb=" CG2 THR G 126 " pdb=" CB THR G 126 " pdb=" HB THR G 126 " ideal model delta sigma weight residual 108.00 80.86 27.14 3.00e+00 1.11e-01 8.19e+01 angle pdb=" CG2 THR E 126 " pdb=" CB THR E 126 " pdb=" HB THR E 126 " ideal model delta sigma weight residual 108.00 80.87 27.13 3.00e+00 1.11e-01 8.18e+01 angle pdb=" CG2 THR C 126 " pdb=" CB THR C 126 " pdb=" HB THR C 126 " ideal model delta sigma weight residual 108.00 80.87 27.13 3.00e+00 1.11e-01 8.18e+01 angle pdb=" CG2 THR A 126 " pdb=" CB THR A 126 " pdb=" HB THR A 126 " ideal model delta sigma weight residual 108.00 80.90 27.10 3.00e+00 1.11e-01 8.16e+01 angle pdb=" CG2 THR H 126 " pdb=" CB THR H 126 " pdb=" HB THR H 126 " ideal model delta sigma weight residual 108.00 80.90 27.10 3.00e+00 1.11e-01 8.16e+01 ... (remaining 35505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9034 17.85 - 35.71: 1026 35.71 - 53.56: 255 53.56 - 71.41: 35 71.41 - 89.26: 40 Dihedral angle restraints: 10390 sinusoidal: 5110 harmonic: 5280 Sorted by residual: dihedral pdb=" CB CYS H 36 " pdb=" SG CYS H 36 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.49 -31.49 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CB CYS C 36 " pdb=" SG CYS C 36 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.46 -31.46 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS A 97 " pdb=" CB CYS A 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.46 -31.46 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 10387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 1900 0.285 - 0.569: 0 0.569 - 0.854: 0 0.854 - 1.139: 0 1.139 - 1.424: 5 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CB THR H 126 " pdb=" CA THR H 126 " pdb=" OG1 THR H 126 " pdb=" CG2 THR H 126 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CB THR A 126 " pdb=" CA THR A 126 " pdb=" OG1 THR A 126 " pdb=" CG2 THR A 126 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.06e+01 chirality pdb=" CB THR E 126 " pdb=" CA THR E 126 " pdb=" OG1 THR E 126 " pdb=" CG2 THR E 126 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.06e+01 ... (remaining 1902 not shown) Planarity restraints: 3195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 145 " -0.294 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CG ASN C 145 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 145 " 0.284 2.00e-02 2.50e+03 pdb=" ND2 ASN C 145 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 145 " 0.473 2.00e-02 2.50e+03 pdb="HD22 ASN C 145 " -0.488 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 145 " 0.294 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CG ASN H 145 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN H 145 " -0.284 2.00e-02 2.50e+03 pdb=" ND2 ASN H 145 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN H 145 " -0.473 2.00e-02 2.50e+03 pdb="HD22 ASN H 145 " 0.488 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 145 " -0.294 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CG ASN G 145 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN G 145 " 0.284 2.00e-02 2.50e+03 pdb=" ND2 ASN G 145 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN G 145 " 0.473 2.00e-02 2.50e+03 pdb="HD22 ASN G 145 " -0.488 2.00e-02 2.50e+03 ... (remaining 3192 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 797 2.17 - 2.78: 32850 2.78 - 3.38: 50145 3.38 - 3.99: 64741 3.99 - 4.60: 97437 Nonbonded interactions: 245970 Sorted by model distance: nonbonded pdb=" OE1 GLU H 130 " pdb=" H GLU H 130 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLU G 130 " pdb=" H GLU G 130 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLU A 130 " pdb=" H GLU A 130 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLU C 130 " pdb=" H GLU C 130 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLU E 130 " pdb=" H GLU E 130 " model vdw 1.559 2.450 ... (remaining 245965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.265 12810 Z= 0.476 Angle : 0.989 11.387 17395 Z= 0.615 Chirality : 0.090 1.424 1905 Planarity : 0.006 0.072 2225 Dihedral : 15.422 89.264 4595 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.18), residues: 1580 helix: -0.66 (0.74), residues: 45 sheet: -1.78 (0.19), residues: 655 loop : -3.13 (0.16), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 67 TYR 0.005 0.001 TYR G 40 PHE 0.012 0.002 PHE A 164 TRP 0.009 0.001 TRP E 110 HIS 0.004 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00561 (12805) covalent geometry : angle 0.97365 (17385) SS BOND : bond 0.26493 ( 5) SS BOND : angle 7.36720 ( 10) hydrogen bonds : bond 0.15453 ( 350) hydrogen bonds : angle 7.00976 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8617 (tp30) cc_final: 0.8162 (tp30) REVERT: A 65 ILE cc_start: 0.9157 (mt) cc_final: 0.8920 (tt) REVERT: A 133 ILE cc_start: 0.9407 (mp) cc_final: 0.9193 (mp) REVERT: B 83 VAL cc_start: 0.8652 (t) cc_final: 0.8445 (t) REVERT: C 62 GLU cc_start: 0.8428 (tp30) cc_final: 0.8044 (tp30) REVERT: C 65 ILE cc_start: 0.9206 (mt) cc_final: 0.8982 (tt) REVERT: C 170 GLU cc_start: 0.8780 (mp0) cc_final: 0.8561 (mp0) REVERT: D 15 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7779 (mm-40) REVERT: D 46 ARG cc_start: 0.8449 (ptm160) cc_final: 0.8059 (ptm160) REVERT: D 83 VAL cc_start: 0.8687 (t) cc_final: 0.8474 (t) REVERT: D 95 TYR cc_start: 0.7966 (m-80) cc_final: 0.7390 (m-10) REVERT: D 101 ASN cc_start: 0.8056 (t0) cc_final: 0.7775 (m-40) REVERT: E 62 GLU cc_start: 0.8614 (tp30) cc_final: 0.8220 (tp30) REVERT: E 65 ILE cc_start: 0.9209 (mt) cc_final: 0.8974 (tt) REVERT: E 170 GLU cc_start: 0.8703 (mp0) cc_final: 0.8411 (mp0) REVERT: F 46 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8286 (ptm160) REVERT: F 83 VAL cc_start: 0.8696 (t) cc_final: 0.8461 (t) REVERT: G 38 HIS cc_start: 0.5913 (t70) cc_final: 0.5612 (t70) REVERT: G 65 ILE cc_start: 0.9199 (mt) cc_final: 0.8996 (tt) REVERT: I 46 ARG cc_start: 0.8656 (ptm160) cc_final: 0.8266 (ptm160) REVERT: I 95 TYR cc_start: 0.8063 (m-80) cc_final: 0.7610 (m-10) REVERT: H 62 GLU cc_start: 0.8560 (tp30) cc_final: 0.8337 (tp30) REVERT: H 65 ILE cc_start: 0.9118 (mt) cc_final: 0.8882 (tt) REVERT: H 170 GLU cc_start: 0.8715 (mp0) cc_final: 0.8496 (mp0) REVERT: J 46 ARG cc_start: 0.8585 (ptm160) cc_final: 0.8297 (ptm160) REVERT: J 86 LEU cc_start: 0.8901 (tp) cc_final: 0.8665 (tt) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2061 time to fit residues: 134.5516 Evaluate side-chains 350 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.077190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.057029 restraints weight = 85194.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.060261 restraints weight = 33513.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.062479 restraints weight = 17919.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.063953 restraints weight = 11199.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.064795 restraints weight = 7832.401| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12810 Z= 0.216 Angle : 0.643 11.367 17395 Z= 0.351 Chirality : 0.084 1.412 1905 Planarity : 0.005 0.067 2225 Dihedral : 6.529 83.528 1735 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.19), residues: 1580 helix: 0.17 (0.83), residues: 45 sheet: -1.35 (0.22), residues: 555 loop : -3.06 (0.16), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 46 TYR 0.014 0.001 TYR I 38 PHE 0.019 0.001 PHE A 180 TRP 0.009 0.001 TRP H 205 HIS 0.011 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00464 (12805) covalent geometry : angle 0.64319 (17385) SS BOND : bond 0.00549 ( 5) SS BOND : angle 0.97954 ( 10) hydrogen bonds : bond 0.04914 ( 350) hydrogen bonds : angle 6.65873 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8721 (pp20) cc_final: 0.8458 (pp20) REVERT: A 16 ASP cc_start: 0.8934 (p0) cc_final: 0.8442 (p0) REVERT: A 62 GLU cc_start: 0.8610 (tp30) cc_final: 0.7876 (tp30) REVERT: A 65 ILE cc_start: 0.9439 (mt) cc_final: 0.9238 (tt) REVERT: A 80 SER cc_start: 0.9119 (m) cc_final: 0.8475 (p) REVERT: C 16 ASP cc_start: 0.8883 (p0) cc_final: 0.8442 (p0) REVERT: C 80 SER cc_start: 0.9191 (m) cc_final: 0.8635 (p) REVERT: D 22 LEU cc_start: 0.9338 (mp) cc_final: 0.9121 (mt) REVERT: E 16 ASP cc_start: 0.8999 (p0) cc_final: 0.8688 (p0) REVERT: E 62 GLU cc_start: 0.8641 (tp30) cc_final: 0.8101 (tp30) REVERT: E 80 SER cc_start: 0.9157 (m) cc_final: 0.8458 (p) REVERT: E 170 GLU cc_start: 0.8754 (mp0) cc_final: 0.8442 (mp0) REVERT: G 80 SER cc_start: 0.9198 (m) cc_final: 0.8483 (p) REVERT: I 22 LEU cc_start: 0.9398 (mt) cc_final: 0.9196 (mt) REVERT: I 89 GLU cc_start: 0.8587 (pm20) cc_final: 0.8348 (pm20) REVERT: H 16 ASP cc_start: 0.8938 (p0) cc_final: 0.8553 (p0) REVERT: H 80 SER cc_start: 0.9163 (m) cc_final: 0.8522 (p) REVERT: J 39 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: J 83 VAL cc_start: 0.8712 (t) cc_final: 0.8134 (t) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2052 time to fit residues: 114.5083 Evaluate side-chains 305 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.057853 restraints weight = 83775.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.061174 restraints weight = 33190.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.063451 restraints weight = 17686.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.064855 restraints weight = 11018.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065891 restraints weight = 7763.716| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12810 Z= 0.121 Angle : 0.570 11.368 17395 Z= 0.313 Chirality : 0.084 1.417 1905 Planarity : 0.004 0.052 2225 Dihedral : 6.262 81.247 1735 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.19), residues: 1580 helix: 0.71 (0.83), residues: 45 sheet: -1.14 (0.22), residues: 555 loop : -2.79 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 46 TYR 0.011 0.001 TYR J 38 PHE 0.014 0.001 PHE F 100 TRP 0.013 0.001 TRP C 205 HIS 0.009 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00271 (12805) covalent geometry : angle 0.57029 (17385) SS BOND : bond 0.00228 ( 5) SS BOND : angle 0.60581 ( 10) hydrogen bonds : bond 0.04267 ( 350) hydrogen bonds : angle 6.31068 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8681 (pp20) cc_final: 0.8457 (pp20) REVERT: A 16 ASP cc_start: 0.8964 (p0) cc_final: 0.8521 (p0) REVERT: A 62 GLU cc_start: 0.8437 (tp30) cc_final: 0.7765 (tp30) REVERT: A 80 SER cc_start: 0.9202 (m) cc_final: 0.8753 (p) REVERT: B 47 GLU cc_start: 0.8169 (pp20) cc_final: 0.7912 (pp20) REVERT: B 83 VAL cc_start: 0.8806 (t) cc_final: 0.8299 (t) REVERT: B 89 GLU cc_start: 0.8688 (pm20) cc_final: 0.8432 (pm20) REVERT: C 14 GLU cc_start: 0.8603 (pp20) cc_final: 0.8335 (pp20) REVERT: C 16 ASP cc_start: 0.9042 (p0) cc_final: 0.8612 (p0) REVERT: C 62 GLU cc_start: 0.8395 (tp30) cc_final: 0.7712 (tp30) REVERT: C 80 SER cc_start: 0.9209 (m) cc_final: 0.8714 (p) REVERT: C 169 ASP cc_start: 0.8920 (p0) cc_final: 0.8571 (p0) REVERT: C 195 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7609 (mm-40) REVERT: D 83 VAL cc_start: 0.8718 (t) cc_final: 0.8153 (t) REVERT: D 89 GLU cc_start: 0.8593 (pm20) cc_final: 0.8339 (pm20) REVERT: E 16 ASP cc_start: 0.9070 (p0) cc_final: 0.8663 (p0) REVERT: E 80 SER cc_start: 0.9171 (m) cc_final: 0.8729 (p) REVERT: F 47 GLU cc_start: 0.7997 (pp20) cc_final: 0.7782 (pp20) REVERT: F 83 VAL cc_start: 0.8813 (t) cc_final: 0.8261 (t) REVERT: F 89 GLU cc_start: 0.8620 (pm20) cc_final: 0.8389 (pm20) REVERT: G 16 ASP cc_start: 0.8946 (p0) cc_final: 0.8638 (p0) REVERT: G 38 HIS cc_start: 0.7136 (t70) cc_final: 0.6898 (t70) REVERT: G 80 SER cc_start: 0.9260 (m) cc_final: 0.8765 (p) REVERT: I 47 GLU cc_start: 0.8112 (pp20) cc_final: 0.7875 (pp20) REVERT: I 83 VAL cc_start: 0.8781 (t) cc_final: 0.8267 (t) REVERT: H 16 ASP cc_start: 0.9022 (p0) cc_final: 0.8599 (p0) REVERT: H 80 SER cc_start: 0.9114 (m) cc_final: 0.8711 (p) REVERT: H 81 GLU cc_start: 0.8536 (pm20) cc_final: 0.8223 (pm20) REVERT: J 39 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7888 (ttm-80) REVERT: J 89 GLU cc_start: 0.8708 (pm20) cc_final: 0.8467 (pm20) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.1880 time to fit residues: 104.7372 Evaluate side-chains 313 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.057379 restraints weight = 83336.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.060361 restraints weight = 32764.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.062406 restraints weight = 17368.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063746 restraints weight = 10771.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.064589 restraints weight = 7618.801| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12810 Z= 0.168 Angle : 0.586 11.421 17395 Z= 0.320 Chirality : 0.083 1.422 1905 Planarity : 0.004 0.046 2225 Dihedral : 6.208 78.009 1735 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.53 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.20), residues: 1580 helix: 0.81 (0.83), residues: 45 sheet: -1.31 (0.23), residues: 495 loop : -2.61 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 104 TYR 0.012 0.001 TYR G 54 PHE 0.014 0.001 PHE A 180 TRP 0.014 0.001 TRP A 205 HIS 0.010 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00371 (12805) covalent geometry : angle 0.58580 (17385) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.65768 ( 10) hydrogen bonds : bond 0.04239 ( 350) hydrogen bonds : angle 6.23595 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9057 (p0) cc_final: 0.8669 (p0) REVERT: A 62 GLU cc_start: 0.8350 (tp30) cc_final: 0.8017 (tp30) REVERT: A 80 SER cc_start: 0.9271 (m) cc_final: 0.8909 (p) REVERT: B 5 GLN cc_start: 0.9453 (tp40) cc_final: 0.9232 (tp40) REVERT: B 22 LEU cc_start: 0.9225 (mm) cc_final: 0.8983 (mm) REVERT: B 47 GLU cc_start: 0.8090 (pp20) cc_final: 0.7814 (pp20) REVERT: C 14 GLU cc_start: 0.8703 (pp20) cc_final: 0.8479 (pp20) REVERT: C 16 ASP cc_start: 0.9080 (p0) cc_final: 0.8705 (p0) REVERT: C 62 GLU cc_start: 0.8362 (tp30) cc_final: 0.7824 (tp30) REVERT: C 80 SER cc_start: 0.9318 (m) cc_final: 0.8807 (p) REVERT: D 21 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8209 (mmm-85) REVERT: D 22 LEU cc_start: 0.9182 (mm) cc_final: 0.8972 (mm) REVERT: D 47 GLU cc_start: 0.8131 (pp20) cc_final: 0.7913 (pp20) REVERT: E 16 ASP cc_start: 0.9104 (p0) cc_final: 0.8699 (p0) REVERT: E 80 SER cc_start: 0.9245 (m) cc_final: 0.8830 (p) REVERT: F 22 LEU cc_start: 0.9206 (mm) cc_final: 0.8945 (mm) REVERT: F 47 GLU cc_start: 0.8088 (pp20) cc_final: 0.7813 (pp20) REVERT: G 16 ASP cc_start: 0.9042 (p0) cc_final: 0.8731 (p0) REVERT: G 80 SER cc_start: 0.9363 (m) cc_final: 0.8941 (p) REVERT: G 170 GLU cc_start: 0.8722 (mp0) cc_final: 0.8485 (mp0) REVERT: H 16 ASP cc_start: 0.9097 (p0) cc_final: 0.8662 (p0) REVERT: H 80 SER cc_start: 0.9170 (m) cc_final: 0.8661 (p) REVERT: J 22 LEU cc_start: 0.9136 (mm) cc_final: 0.8905 (mm) REVERT: J 39 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: J 47 GLU cc_start: 0.8109 (pp20) cc_final: 0.7843 (pp20) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.1736 time to fit residues: 97.8327 Evaluate side-chains 305 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 45 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.074196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.055044 restraints weight = 83899.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.057937 restraints weight = 33750.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.059931 restraints weight = 18271.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.061261 restraints weight = 11516.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.062058 restraints weight = 8192.207| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12810 Z= 0.248 Angle : 0.663 11.487 17395 Z= 0.362 Chirality : 0.084 1.429 1905 Planarity : 0.004 0.043 2225 Dihedral : 6.358 73.242 1735 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.97 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.20), residues: 1580 helix: 0.82 (0.84), residues: 45 sheet: -1.16 (0.23), residues: 520 loop : -2.81 (0.17), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 104 TYR 0.013 0.001 TYR G 54 PHE 0.016 0.002 PHE A 180 TRP 0.011 0.001 TRP G 205 HIS 0.007 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00548 (12805) covalent geometry : angle 0.66272 (17385) SS BOND : bond 0.00539 ( 5) SS BOND : angle 0.76957 ( 10) hydrogen bonds : bond 0.04702 ( 350) hydrogen bonds : angle 6.34100 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9075 (p0) cc_final: 0.8775 (p0) REVERT: A 62 GLU cc_start: 0.8072 (tp30) cc_final: 0.7725 (tp30) REVERT: A 80 SER cc_start: 0.9338 (m) cc_final: 0.9056 (p) REVERT: A 193 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6657 (tm-30) REVERT: B 22 LEU cc_start: 0.9250 (mm) cc_final: 0.8917 (mm) REVERT: C 16 ASP cc_start: 0.9057 (p0) cc_final: 0.8787 (p0) REVERT: C 80 SER cc_start: 0.9404 (m) cc_final: 0.9023 (p) REVERT: C 170 GLU cc_start: 0.8741 (mp0) cc_final: 0.8529 (mp0) REVERT: D 22 LEU cc_start: 0.9198 (mm) cc_final: 0.8863 (mm) REVERT: E 16 ASP cc_start: 0.9145 (p0) cc_final: 0.8695 (p0) REVERT: E 80 SER cc_start: 0.9353 (m) cc_final: 0.9083 (p) REVERT: F 22 LEU cc_start: 0.9248 (mm) cc_final: 0.8916 (mm) REVERT: F 54 ASN cc_start: 0.9074 (t0) cc_final: 0.8809 (t0) REVERT: G 16 ASP cc_start: 0.9073 (p0) cc_final: 0.8822 (p0) REVERT: G 65 ILE cc_start: 0.9513 (mt) cc_final: 0.9290 (tt) REVERT: G 80 SER cc_start: 0.9416 (m) cc_final: 0.9124 (p) REVERT: G 170 GLU cc_start: 0.8721 (mp0) cc_final: 0.8468 (mp0) REVERT: H 16 ASP cc_start: 0.9109 (p0) cc_final: 0.8705 (p0) REVERT: H 80 SER cc_start: 0.9319 (m) cc_final: 0.8942 (p) REVERT: H 170 GLU cc_start: 0.8744 (mp0) cc_final: 0.8463 (mp0) REVERT: J 22 LEU cc_start: 0.9162 (mm) cc_final: 0.8836 (mm) REVERT: J 47 GLU cc_start: 0.8057 (pp20) cc_final: 0.7839 (pp20) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1836 time to fit residues: 99.6593 Evaluate side-chains 283 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.055126 restraints weight = 84352.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.058290 restraints weight = 33598.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.060413 restraints weight = 18037.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.061864 restraints weight = 11390.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.062773 restraints weight = 8031.849| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12810 Z= 0.177 Angle : 0.609 11.511 17395 Z= 0.334 Chirality : 0.084 1.435 1905 Planarity : 0.004 0.034 2225 Dihedral : 6.101 69.531 1735 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.96 % Favored : 92.72 % Rotamer: Outliers : 0.07 % Allowed : 1.68 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.20), residues: 1580 helix: 1.05 (0.85), residues: 45 sheet: -1.24 (0.25), residues: 445 loop : -2.67 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.013 0.001 TYR A 73 PHE 0.015 0.001 PHE A 180 TRP 0.013 0.001 TRP G 205 HIS 0.008 0.002 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00389 (12805) covalent geometry : angle 0.60852 (17385) SS BOND : bond 0.00360 ( 5) SS BOND : angle 0.67303 ( 10) hydrogen bonds : bond 0.04264 ( 350) hydrogen bonds : angle 6.13472 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9145 (p0) cc_final: 0.8862 (p0) REVERT: A 56 THR cc_start: 0.8691 (p) cc_final: 0.7898 (p) REVERT: A 80 SER cc_start: 0.9344 (m) cc_final: 0.9123 (p) REVERT: A 193 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 22 LEU cc_start: 0.9269 (mm) cc_final: 0.8967 (mm) REVERT: B 98 VAL cc_start: 0.8398 (p) cc_final: 0.8188 (p) REVERT: C 16 ASP cc_start: 0.9098 (p0) cc_final: 0.8835 (p0) REVERT: C 47 ARG cc_start: 0.8392 (ptt180) cc_final: 0.7760 (ptt180) REVERT: C 56 THR cc_start: 0.8776 (p) cc_final: 0.8187 (p) REVERT: C 80 SER cc_start: 0.9381 (m) cc_final: 0.8978 (p) REVERT: D 22 LEU cc_start: 0.9227 (mm) cc_final: 0.8928 (mm) REVERT: D 38 TYR cc_start: 0.9113 (m-80) cc_final: 0.8876 (m-80) REVERT: E 14 GLU cc_start: 0.8874 (pp20) cc_final: 0.8667 (pp20) REVERT: E 16 ASP cc_start: 0.9232 (p0) cc_final: 0.8795 (p0) REVERT: E 56 THR cc_start: 0.8815 (p) cc_final: 0.8327 (p) REVERT: E 80 SER cc_start: 0.9370 (m) cc_final: 0.9134 (p) REVERT: E 170 GLU cc_start: 0.8793 (mp0) cc_final: 0.8460 (mp0) REVERT: F 22 LEU cc_start: 0.9247 (mm) cc_final: 0.8956 (mm) REVERT: G 16 ASP cc_start: 0.9121 (p0) cc_final: 0.8868 (p0) REVERT: G 80 SER cc_start: 0.9459 (m) cc_final: 0.9169 (p) REVERT: G 170 GLU cc_start: 0.8761 (mp0) cc_final: 0.8504 (mp0) REVERT: I 48 LEU cc_start: 0.8920 (tt) cc_final: 0.8626 (tt) REVERT: I 93 ILE cc_start: 0.8911 (mm) cc_final: 0.8680 (mm) REVERT: H 16 ASP cc_start: 0.9181 (p0) cc_final: 0.8753 (p0) REVERT: H 80 SER cc_start: 0.9017 (m) cc_final: 0.8622 (p) REVERT: H 81 GLU cc_start: 0.8298 (pp20) cc_final: 0.7677 (pp20) REVERT: H 82 ILE cc_start: 0.8717 (mm) cc_final: 0.8239 (mm) REVERT: H 85 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 170 GLU cc_start: 0.8776 (mp0) cc_final: 0.8475 (mp0) REVERT: J 22 LEU cc_start: 0.9131 (mm) cc_final: 0.8826 (mm) REVERT: J 47 GLU cc_start: 0.7984 (pp20) cc_final: 0.7727 (pp20) REVERT: J 98 VAL cc_start: 0.8262 (p) cc_final: 0.8021 (p) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.1808 time to fit residues: 102.2231 Evaluate side-chains 291 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 GLN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN J 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.074748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.054639 restraints weight = 85101.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.057790 restraints weight = 34386.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.059925 restraints weight = 18618.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.061366 restraints weight = 11779.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.062232 restraints weight = 8348.007| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12810 Z= 0.239 Angle : 0.656 11.529 17395 Z= 0.358 Chirality : 0.084 1.432 1905 Planarity : 0.003 0.029 2225 Dihedral : 6.069 65.286 1735 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.86 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.20), residues: 1580 helix: 0.86 (0.84), residues: 45 sheet: -1.13 (0.24), residues: 500 loop : -2.80 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 39 TYR 0.014 0.001 TYR A 54 PHE 0.017 0.002 PHE A 180 TRP 0.010 0.001 TRP G 205 HIS 0.011 0.003 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00529 (12805) covalent geometry : angle 0.65562 (17385) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.79114 ( 10) hydrogen bonds : bond 0.04527 ( 350) hydrogen bonds : angle 6.17201 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9120 (p0) cc_final: 0.8862 (p0) REVERT: B 22 LEU cc_start: 0.9250 (mm) cc_final: 0.8929 (mm) REVERT: C 16 ASP cc_start: 0.9074 (p0) cc_final: 0.8828 (p0) REVERT: C 80 SER cc_start: 0.9360 (m) cc_final: 0.8962 (p) REVERT: D 22 LEU cc_start: 0.9159 (mm) cc_final: 0.8827 (mm) REVERT: D 38 TYR cc_start: 0.9159 (m-80) cc_final: 0.8872 (m-80) REVERT: E 16 ASP cc_start: 0.9209 (p0) cc_final: 0.8816 (p0) REVERT: E 47 ARG cc_start: 0.8372 (ptt180) cc_final: 0.8128 (ptt180) REVERT: F 22 LEU cc_start: 0.9211 (mm) cc_final: 0.8886 (mm) REVERT: G 16 ASP cc_start: 0.9071 (p0) cc_final: 0.8825 (p0) REVERT: G 80 SER cc_start: 0.9432 (m) cc_final: 0.9212 (p) REVERT: I 93 ILE cc_start: 0.8932 (mm) cc_final: 0.8704 (mm) REVERT: H 16 ASP cc_start: 0.9189 (p0) cc_final: 0.8805 (p0) REVERT: H 80 SER cc_start: 0.9114 (m) cc_final: 0.8822 (p) REVERT: H 81 GLU cc_start: 0.8429 (pp20) cc_final: 0.7901 (pp20) REVERT: H 82 ILE cc_start: 0.8758 (mm) cc_final: 0.8281 (mm) REVERT: H 170 GLU cc_start: 0.8762 (mp0) cc_final: 0.8486 (mp0) REVERT: J 22 LEU cc_start: 0.9090 (mm) cc_final: 0.8781 (mm) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1963 time to fit residues: 100.5778 Evaluate side-chains 278 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 124 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.055462 restraints weight = 84343.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.058665 restraints weight = 33622.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.060854 restraints weight = 18019.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.062283 restraints weight = 11253.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.063281 restraints weight = 7964.698| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12810 Z= 0.155 Angle : 0.611 11.472 17395 Z= 0.333 Chirality : 0.084 1.431 1905 Planarity : 0.003 0.027 2225 Dihedral : 5.826 60.772 1735 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.15 % Favored : 92.53 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.20), residues: 1580 helix: 1.19 (0.86), residues: 45 sheet: -1.14 (0.26), residues: 445 loop : -2.57 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.014 0.001 TYR A 54 PHE 0.014 0.001 PHE A 180 TRP 0.010 0.001 TRP H 205 HIS 0.006 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00350 (12805) covalent geometry : angle 0.61067 (17385) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.72376 ( 10) hydrogen bonds : bond 0.04069 ( 350) hydrogen bonds : angle 5.96490 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9144 (p0) cc_final: 0.8882 (p0) REVERT: A 62 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6955 (mm-30) REVERT: B 22 LEU cc_start: 0.9248 (mm) cc_final: 0.8905 (mm) REVERT: C 16 ASP cc_start: 0.9098 (p0) cc_final: 0.8848 (p0) REVERT: C 40 TYR cc_start: 0.8632 (t80) cc_final: 0.8127 (t80) REVERT: C 80 SER cc_start: 0.9364 (m) cc_final: 0.9101 (p) REVERT: D 22 LEU cc_start: 0.9196 (mm) cc_final: 0.8888 (mm) REVERT: D 38 TYR cc_start: 0.9165 (m-80) cc_final: 0.8881 (m-80) REVERT: D 83 VAL cc_start: 0.8201 (t) cc_final: 0.7908 (t) REVERT: D 98 VAL cc_start: 0.8143 (p) cc_final: 0.7918 (p) REVERT: E 16 ASP cc_start: 0.9233 (p0) cc_final: 0.8835 (p0) REVERT: F 22 LEU cc_start: 0.9238 (mm) cc_final: 0.8918 (mm) REVERT: G 16 ASP cc_start: 0.9138 (p0) cc_final: 0.8898 (p0) REVERT: G 80 SER cc_start: 0.9430 (m) cc_final: 0.9184 (p) REVERT: G 170 GLU cc_start: 0.8790 (mp0) cc_final: 0.8537 (mp0) REVERT: I 93 ILE cc_start: 0.8907 (mm) cc_final: 0.8683 (mm) REVERT: H 16 ASP cc_start: 0.9206 (p0) cc_final: 0.8812 (p0) REVERT: H 56 THR cc_start: 0.8752 (p) cc_final: 0.8349 (p) REVERT: H 80 SER cc_start: 0.9084 (m) cc_final: 0.8797 (p) REVERT: H 81 GLU cc_start: 0.8477 (pp20) cc_final: 0.7933 (pp20) REVERT: H 82 ILE cc_start: 0.8727 (mm) cc_final: 0.8243 (mm) REVERT: H 170 GLU cc_start: 0.8785 (mp0) cc_final: 0.8488 (mp0) REVERT: J 22 LEU cc_start: 0.9098 (mm) cc_final: 0.8720 (mm) REVERT: J 98 VAL cc_start: 0.8237 (p) cc_final: 0.8018 (p) outliers start: 1 outliers final: 1 residues processed: 359 average time/residue: 0.1864 time to fit residues: 97.9314 Evaluate side-chains 287 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.054608 restraints weight = 84125.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.057762 restraints weight = 33551.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.059925 restraints weight = 18030.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.061322 restraints weight = 11332.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.062290 restraints weight = 7986.447| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12810 Z= 0.217 Angle : 0.648 11.526 17395 Z= 0.353 Chirality : 0.084 1.432 1905 Planarity : 0.003 0.029 2225 Dihedral : 5.790 54.652 1735 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 30.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.44 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.20), residues: 1580 helix: 0.94 (0.84), residues: 45 sheet: -1.11 (0.26), residues: 445 loop : -2.62 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 104 TYR 0.015 0.001 TYR H 54 PHE 0.017 0.002 PHE A 180 TRP 0.009 0.001 TRP G 205 HIS 0.014 0.003 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00482 (12805) covalent geometry : angle 0.64807 (17385) SS BOND : bond 0.00471 ( 5) SS BOND : angle 0.78773 ( 10) hydrogen bonds : bond 0.04357 ( 350) hydrogen bonds : angle 6.06028 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9118 (p0) cc_final: 0.8877 (p0) REVERT: B 22 LEU cc_start: 0.9185 (mm) cc_final: 0.8818 (mm) REVERT: B 83 VAL cc_start: 0.8400 (t) cc_final: 0.8007 (t) REVERT: C 16 ASP cc_start: 0.9083 (p0) cc_final: 0.8850 (p0) REVERT: C 80 SER cc_start: 0.9390 (m) cc_final: 0.9151 (p) REVERT: D 22 LEU cc_start: 0.9116 (mm) cc_final: 0.8776 (mm) REVERT: E 16 ASP cc_start: 0.9210 (p0) cc_final: 0.8846 (p0) REVERT: F 22 LEU cc_start: 0.9170 (mm) cc_final: 0.8773 (mm) REVERT: F 83 VAL cc_start: 0.8372 (t) cc_final: 0.7997 (t) REVERT: G 16 ASP cc_start: 0.9097 (p0) cc_final: 0.8853 (p0) REVERT: G 80 SER cc_start: 0.9412 (m) cc_final: 0.9202 (p) REVERT: I 83 VAL cc_start: 0.8551 (t) cc_final: 0.8166 (t) REVERT: I 93 ILE cc_start: 0.8961 (mm) cc_final: 0.8740 (mm) REVERT: H 16 ASP cc_start: 0.9173 (p0) cc_final: 0.8802 (p0) REVERT: H 56 THR cc_start: 0.8688 (p) cc_final: 0.8345 (p) REVERT: H 62 GLU cc_start: 0.8896 (tp30) cc_final: 0.8514 (tp30) REVERT: H 80 SER cc_start: 0.9129 (m) cc_final: 0.8864 (p) REVERT: H 81 GLU cc_start: 0.8483 (pp20) cc_final: 0.8006 (pp20) REVERT: H 82 ILE cc_start: 0.8730 (mm) cc_final: 0.8206 (mm) REVERT: H 170 GLU cc_start: 0.8778 (mp0) cc_final: 0.8505 (mp0) REVERT: J 22 LEU cc_start: 0.9029 (mm) cc_final: 0.8634 (mm) REVERT: J 83 VAL cc_start: 0.8317 (t) cc_final: 0.7901 (t) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1711 time to fit residues: 89.2927 Evaluate side-chains 293 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 74 ASN F 54 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.056990 restraints weight = 81856.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.060069 restraints weight = 32596.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.062111 restraints weight = 17339.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.063478 restraints weight = 10895.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.064298 restraints weight = 7734.125| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12810 Z= 0.106 Angle : 0.598 11.423 17395 Z= 0.325 Chirality : 0.084 1.425 1905 Planarity : 0.003 0.032 2225 Dihedral : 5.435 48.445 1735 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.39 % Favored : 93.29 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.20), residues: 1580 helix: 1.31 (0.86), residues: 45 sheet: -1.00 (0.26), residues: 445 loop : -2.45 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.013 0.001 TYR H 54 PHE 0.011 0.001 PHE A 180 TRP 0.015 0.001 TRP G 205 HIS 0.009 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00247 (12805) covalent geometry : angle 0.59786 (17385) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.66052 ( 10) hydrogen bonds : bond 0.03766 ( 350) hydrogen bonds : angle 5.78500 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9110 (p0) cc_final: 0.8852 (p0) REVERT: B 22 LEU cc_start: 0.9190 (mm) cc_final: 0.8832 (mm) REVERT: B 83 VAL cc_start: 0.8653 (t) cc_final: 0.8285 (t) REVERT: C 16 ASP cc_start: 0.9061 (p0) cc_final: 0.8819 (p0) REVERT: C 80 SER cc_start: 0.9314 (m) cc_final: 0.9099 (p) REVERT: C 170 GLU cc_start: 0.8749 (mp0) cc_final: 0.8532 (mp0) REVERT: D 22 LEU cc_start: 0.9120 (mm) cc_final: 0.8783 (mm) REVERT: D 98 VAL cc_start: 0.8139 (p) cc_final: 0.7938 (p) REVERT: E 16 ASP cc_start: 0.9185 (p0) cc_final: 0.8796 (p0) REVERT: F 21 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8389 (mmm-85) REVERT: F 22 LEU cc_start: 0.9186 (mm) cc_final: 0.8854 (mm) REVERT: F 83 VAL cc_start: 0.8380 (t) cc_final: 0.8019 (t) REVERT: F 98 VAL cc_start: 0.8141 (p) cc_final: 0.7938 (p) REVERT: G 16 ASP cc_start: 0.9090 (p0) cc_final: 0.8847 (p0) REVERT: G 170 GLU cc_start: 0.8776 (mp0) cc_final: 0.8530 (mp0) REVERT: I 83 VAL cc_start: 0.8713 (t) cc_final: 0.8419 (t) REVERT: I 93 ILE cc_start: 0.9015 (mm) cc_final: 0.8795 (mm) REVERT: H 16 ASP cc_start: 0.9146 (p0) cc_final: 0.8753 (p0) REVERT: H 40 TYR cc_start: 0.8532 (t80) cc_final: 0.8288 (t80) REVERT: H 56 THR cc_start: 0.8704 (p) cc_final: 0.8476 (p) REVERT: H 62 GLU cc_start: 0.8622 (tp30) cc_final: 0.8370 (tp30) REVERT: H 80 SER cc_start: 0.9062 (m) cc_final: 0.8790 (p) REVERT: H 81 GLU cc_start: 0.8434 (pp20) cc_final: 0.8026 (pp20) REVERT: H 82 ILE cc_start: 0.8768 (mm) cc_final: 0.8342 (mm) REVERT: H 170 GLU cc_start: 0.8793 (mp0) cc_final: 0.8430 (mp0) REVERT: J 22 LEU cc_start: 0.9073 (mm) cc_final: 0.8680 (mm) REVERT: J 83 VAL cc_start: 0.8489 (t) cc_final: 0.8118 (t) REVERT: J 98 VAL cc_start: 0.8230 (p) cc_final: 0.8002 (p) outliers start: 2 outliers final: 1 residues processed: 371 average time/residue: 0.1860 time to fit residues: 101.8032 Evaluate side-chains 293 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 70 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN C 38 HIS D 74 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.058060 restraints weight = 81280.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.061171 restraints weight = 32427.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.063251 restraints weight = 17310.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.064699 restraints weight = 10855.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.065354 restraints weight = 7580.966| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12810 Z= 0.099 Angle : 0.594 11.392 17395 Z= 0.321 Chirality : 0.084 1.419 1905 Planarity : 0.003 0.030 2225 Dihedral : 5.055 42.477 1735 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.52 % Favored : 93.29 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1580 helix: 1.30 (0.86), residues: 45 sheet: -0.66 (0.24), residues: 495 loop : -2.47 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.014 0.001 TYR H 54 PHE 0.010 0.001 PHE A 180 TRP 0.008 0.001 TRP G 110 HIS 0.004 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00235 (12805) covalent geometry : angle 0.59368 (17385) SS BOND : bond 0.00181 ( 5) SS BOND : angle 0.61972 ( 10) hydrogen bonds : bond 0.03514 ( 350) hydrogen bonds : angle 5.58779 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.67 seconds wall clock time: 58 minutes 25.07 seconds (3505.07 seconds total)